Version bump. #77
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| # Lingfei Wang, 2022, 2023. All rights reserved. | |
| name: "Container image" | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| paths: | |
| - 'setup.py' | |
| - 'src/**' | |
| - 'bin/**' | |
| - 'utils/docker/**' | |
| - 'doc/scripts/install.sh' | |
| - '.github/workflows/ci-container.yml' | |
| - '.github/actions/dockerhub-build-publish/**' | |
| jobs: | |
| build-cpu: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish pretest version | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish-pretest | |
| with: | |
| registry: lfwa | |
| image: dictys-cpu-dev | |
| test-blood1-cpu: | |
| name: Blood static network unit tests | |
| needs: build-cpu | |
| runs-on: ubuntu-latest | |
| container: | |
| image: lfwa/dictys-cpu-dev | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Get dataset URL | |
| id: zenodo-url-translate | |
| uses: ./.github/actions/zenodo-url-translate | |
| with: | |
| url: https://zenodo.org/records/6858494/files/inference-blood1.tar.xz?download=1 | |
| - name: Test dataset | |
| uses: ./.github/actions/inference-test-dataset | |
| with: | |
| url: ${{ steps.zenodo-url-translate.outputs.url }} | |
| test-path: ci_testspace | |
| makefile: test_static.mk | |
| expected-folder: test/tmp_static_expected | |
| actual-folder: test/tmp_static | |
| expected-h5: test/output/static_expected.h5 | |
| actual-h5: test/output/static.h5 | |
| makefile-params: '{"ENVMODE": "none", "NTH": "2", "DEVICE": "cpu", "GENOME_MACS2": "hs", "JOINT": "0", "KPARAMS-NETWORK-RECONSTRUCT+": " --nstep 10 --nstep_report 3"}' | |
| exclusions: 'reads.bam reads.bai net_weight.tsv.gz net_covfactor.tsv.gz net_meanvar.tsv.gz net_loss.tsv.gz net_stats.tsv.gz' | |
| build-publish-cpu: | |
| needs: test-blood1-cpu | |
| if: ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' ) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish | |
| with: | |
| registry: lfwa | |
| image: dictys-cpu | |
| build-publish-cuda: | |
| needs: test-blood1-cpu | |
| if: false && ( github.ref_name == 'master' ) && ( github.repository == 'pinellolab/dictys' ) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| cuda: [11.3,11.6,11.7] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: local | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USER }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and publish | |
| uses: ./local/.github/actions/dockerhub-build-publish | |
| id: publish | |
| with: | |
| registry: lfwa | |
| cuda: ${{ matrix.cuda }} | |
| image: dictys-cuda{{ matrix.cuda }} |